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First things first, plague isn't exactly nature's way of controlling prairie dogs. Plague (Yersinia pestis) was introduced to North America around 1900 by shipboard rats in San Francisco. It then spread fairly quickly throughout the west from the Pacific to about the 100th meridian. Because the bacteria that causes plague is a fairly young species (~20,000-10,000 years since speciation), and because it isn't native to North America, its virulence in naive populations of susceptible critters can be very high. In prairie dogs, the disease is 100% fatal to exposed animals. Those that manage to survive do so because by chance they were not exposed to the bacterium. Those species that are more densely colonial, especially blacktailed prairie dogs (the most widespread species), often see a population decline on the order of 95% in the first plague incursion, followed by a diminishing stairstep pattern as the colony never quite reaches the previous numbers before the next plague incursion. Given that the current prairie dog acreage is on the order of 2% of historic extent, and that the only remaining large complexes of blacktails are on one National Grassland and three reservations in SD (two of these four are now plague zones), and on this chunk of private land in KS, it's a pretty big deal for plague to come in and knock any one of them into a death spiral.
What limited prairie dog density prior to extensive homesteading was predation by a full cast of critters, precipitation, and density-dependent effects such as intraspecies aggression (infanticide, cannibalism, that sort of thing). With the onset of fenced grazing, we've managed to alter several of those controlling factors. Top-down predator control with coyotes and badgers won't be as effective as top-down predator control with ferrets and swift foxes. High grass growth in years of high precipitation is no longer a limit to prairie dog expansion in the eastern part of their range because ranchers see that grass growth as an opportunity to hammer the hell out of their pastures with as many cattle as they can shoehorn out there. Density-dependent factors still limit how many prairie dogs can share an acre of land, but when landowners neighboring prairie dog towns graze or mow their fields down to a couple inches of stubble, they are essentially telling the prairie dogs on adjoining land "Give me your tired, your poor, your huddled masses..." And of course, because we manage real property the way we do, there is no incentive for landowners to maybe cooperate and rest large chunks of pastureland for years at a time between intensive grazing sessions, to mimic bison disturbance patterns that historically helped shape and move prairie dog towns across the landscape. Not when they can turn a quick profit and socialize the long term costs with federally subsidized drought aid, forage aid, poisoning programs, and the like.
By the way, being in a prairie dog town during an active plague epizootic is not too terribly risky. I've done it myself for long stretches of time, simple precautions will keep anyone safe. What is risky is handling squirrels, mice, rats, cats, and dogs that have been in active plague zones and that may be carrying infected fleas, or worse (in the case of cats especially), that may be able to pass the disease directly to humans. Interestingly, the flea species in the United States are not nearly as effective as plague vectors as some of the east Asian flea species, so while flea bites are an issue, direct transmission through body fluid contact is more of a concern. Bites or scratches from potentially infected carriers in active plague zones need to be brought to the attention of a doctor immediately-not doing so can reduce the chances of recovery very quickly as the disease progresses. A biologist at Grand Canyon contracted plague while performing a necropsy on a mountain lion, apparently didn't mention the possibility of plague to his doctor when he was checked for flu-like symptoms a day or two later, and was dead three days after that. All that can be avoided, however, by not handling suspect animals. Notice that a lot of rats are suddenly dying around your grain bins, and you haven't been poisoning? Might want to have an expert check it out. Notice that your farm cats are all suddenly ill, acting listless, and maybe sneezing bloody mucous? Again, might want to have an expert check it out.
As for poisoning, it's an economic loser unless the town is entirely eradicated. This was somewhat effective during the early decades of the 1900's because the federal government threw ridiculous sums of money into indiscriminate poisoning campaigns across the plains using such extremely effective toxins as strychnine and compound 1080. In fact, the Biological Survey pimped poisoning under the guise of increasing the land's grazing production as a means to justify increasing it's budget. Those toxins are now illegal to use, and the newer toxins are less effective while also requiring extensive labor to pre-bait the zone to be poisoned to accustom prairie dogs to the bait. The reason states like Kansas have or had this home rule law on the books is because their legislature was dominated by the ag lobby from their inception as states, and the idea of "too many prairie dogs" is so ingrained in the local culture that children growing up there will without fail see prairie dogs' only real worth as target practice. Farmer Bob hears that neighboring rancher Joe has a few prairie dogs on his property, and he files a complaint because in his opinion, the only good dog is a dead dog, and he'll be damned if he's gonna give up one blade of grass to Joe's dogs. That's how many people out there see it...prairie dogs are not wildlife, they are someone else's property to be kept on the other side of the fence, and when those prairie dogs roam as they are programmed by evolution to do, the state steps in to protect Bob's property rights...by stepping all over Joe's property rights and billing him for the trouble.
Shooting is no great solution either. I've seen opening day on some of the national grasslands...some guys are good shots and careful with their aim, others not so much. Simple safety aside, not an insignificant number of shooters apparently have no problem taking shots at other wildlife as the opportunity arises...burrowing owls, jackrabbits, harriers, and so on down the list have been poached and left to rot just because they were there. As well, intensive shooting very quickly alters prairie dog behavior and can have as severe an impact on population size as intensive poisoning or even plague. Add that to poisoning and plague pressures on the remaining large complexes in South Dakota and Kansas, and I could very easily see the Fish and Wildlife Service listing black-tailed prairie dogs as threatened upon completion of the review they are currently conducting. If that happens, ESA provisions are going to severely limit poisoning and recreational shooting, and people are going to be forced to manage prairie dogs as wildlife until/unless a plague vaccine or natural resistance to plague can be found. I'm not holding my breath for a vaccine or natural resistance.
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